Search

Abstract Background In 2022, fewer than half of persons with tuberculosis (TB) had access to molecular diagnostic tests for TB due to their high costs. Studies have found that the use of artificial intelligence (AI) software for chest X-ray (CXR) interpretation and sputum specimen pooling can each reduce the cost of testing. We modeled the combination of both strategies to estimate potential savings in consumables that could be used to expand access to molecular diagnostics. Methods We obtained Xpert testing and positivity data segmented into deciles by AI probability scores for TB from the community- and healthcare facility-based active case finding conducted in Bangladesh, Nigeria, Viet Nam, and Zambia. AI scores in the model were based on CAD4TB version 7 (Zambia) and qXR (all other countries). We modeled four ordinal screening and testing approaches involving AI-aided CXR interpretation to indicate individual and pooled testing. Setting a false negative rate of 5%, for each approach we calculated additional and cumulative savings over the baseline of universal Xpert testing, as well as the theoretical expansion in diagnostic coverage. Results In each country, the optimal screening and testing approach was to use AI to rule out testing in deciles with low AI scores and to guide pooled vs individual testing in persons with moderate and high AI scores, respectively. This approach yielded cumulative savings in Xpert tests over baseline ranging from 50.8% in Zambia to 57.5% in Nigeria and 61.5% in Bangladesh and Viet Nam. Using these savings, diagnostic coverage theoretically could be expanded by 34% to 160% across the different approaches and countries. Conclusions Using AI software data generated during CXR interpretation to inform a differentiated pooled testing strategy may optimize TB diagnostic test use, and could extend molecular tests to more people who need them. The optimal AI thresholds and pooled testing strategy varied across countries, which suggests that bespoke screening and testing approaches may be needed for differing populations and settings.

Lack of appropriate early diagnostic tools for drug-resistant tuberculosis (DR-TB) and their incomplete drug susceptibility testing (DST) profiling is concerning for TB disease control. Existing methods, such as phenotypic DST (pDST), are time-consuming, while Xpert MTB/RIF (Xpert) and line probe assay (LPA) are limited to detecting resistance to few drugs. Targeted next-generation sequencing (tNGS) has been recently approved by WHO as an alternative approach for rapid and comprehensive DST. We aimed to investigate the performance and feasibility of tNGS for detecting DR-TB directly from clinical samples in Bangladesh. pDST, LPA and tNGS were performed among 264 sputum samples, either rifampicin-resistant (RR) or rifampicin-sensitive (RS) TB cases confirmed by Xpert assay. Resistotypes of tNGS were compared with pDST, LPA and composite reference standard (CRS, resistant if either pDST or LPA showed a resistant result). tNGS results revealed higher sensitivities for rifampicin (RIF) (99.3%), isoniazid (INH) (96.3%), fluoroquinolones (FQs) (94.4%), and aminoglycosides (AMGs) (100%) but comparatively lower for ethambutol (76.6%), streptomycin (68.7%), ethionamide (56.0%) and pyrazinamide (50.7%) when compared with pDST. The sensitivities of tNGS for INH, RIF, FQs and AMGs were 93.0%, 96.6%, 90.9%, and 100%, respectively and the specificities ranged from 91.3 to 100% when compared with CRS. This proof of concept study, conducted in a high-burden setting demonstrated that tNGS is a valuable tool for identifying DR-TB directly from the clinical specimens. Its feasibility in our laboratory suggests potential implementation and moving tNGS from research settings into clinical settings.

Real-time monitoring and management of lettuce plants, especially during the seedling growth stage, is important in order to protect them from various environmental stresses and to prevent yield loss. Various and similar symptoms may occur as a result of different unfavorable environmental stresses. Visual inspection alone may result in an incorrect and late diagnosis, obstructing subsequent corrective action for the damaged seedlings in an early stage. The purposes of this study were to detect and segment lettuce seedlings from the background of seedling-growing trays using an improved mask R-CNN and to estimate seedling size based on the output of the proposed technique. Lettuce seedling images were taken from a plant factory using an automatic image acquisition tool. The seedlings in the images were 1 to 3 weeks old. An annotation of 1,000 lettuce seedling image datasets was prepared using an online annotation tool. An improved mask R-CNN was implemented using ResNet-101 with CB-Net, which provided enhanced image feature extraction. Transfer learning was used to train the model network with a smaller dataset and reduce the processing time. Bounding boxes and annotations were set as inputs for the training model. Training and test datasets were prepared for the model evaluation. The sizes of the seedlings were determined by applying a binary mask to the output-masked seedling images. The total number of pixels was used to determine the seedling size. The training loss of the selected method was less than 0.20 %. The identification of lettuce seedlings from 150 randomly chosen test photos revealed that the best-fit image had a performance F1 score of 93 %, corresponding to 92 % precision and 95 % recall. A strong linear relationship (R2>0.99) between manual and model-estimated leaf area confirmed the proposed model accuracy throughout the lettuce growth stages. The improved mask R-CNN could detect lettuce seedlings in the tray image background and also extract the leaf area of identified lettuce seedlings.

Pig farming, a vital industry, necessitates proactive measures for early disease detection and crush symptom monitoring to ensure optimum pig health and safety. This review explores advanced thermal sensing technologies and computer vision-based thermal imaging techniques employed for pig disease and piglet crush symptom monitoring on pig farms. Infrared thermography (IRT) is a non-invasive and efficient technology for measuring pig body temperature, providing advantages such as non-destructive, long-distance, and high-sensitivity measurements. Unlike traditional methods, IRT offers a quick and labor-saving approach to acquiring physiological data impacted by environmental temperature, crucial for understanding pig body physiology and metabolism. IRT aids in early disease detection, respiratory health monitoring, and evaluating vaccination effectiveness. Challenges include body surface emissivity variations affecting measurement accuracy. Thermal imaging and deep learning algorithms are used for pig behavior recognition, with the dorsal plane effective for stress detection. Remote health monitoring through thermal imaging, deep learning, and wearable devices facilitates non-invasive assessment of pig health, minimizing medication use. Integration of advanced sensors, thermal imaging, and deep learning shows potential for disease detection and improvement in pig farming, but challenges and ethical considerations must be addressed for successful implementation. This review summarizes the state-of-the-art technologies used in the pig farming industry, including computer vision algorithms such as object detection, image segmentation, and deep learning techniques. It also discusses the benefits and limitations of IRT technology, providing an overview of the current research field. This study provides valuable insights for researchers and farmers regarding IRT application in pig production, highlighting notable approaches and the latest research findings in this field.

Digital adherence technologies are increasingly used to support tuberculosis (TB) treatment adherence. Using microcosting, we estimated healthcare system costs (in 2022 US dollars) of 2 digital adherence technologies, 99DOTS medication sleeves and video-observed therapy (VOT), implemented in demonstration projects during 2018–2021. We also obtained cost estimates for standard directly observed therapy (DOT). Estimated per-person costs of 99DOTS for drug-sensitive TB were $98 in Bangladesh (n = 719), $119 in the Philippines (n = 396), and $174 in Tanzania (n = 976). Estimated per-person costs of VOT were $1,154 in Haiti (87 drug-sensitive), $304 in Moldova (173 drug-sensitive), $452 in Moldova (135 drug-resistant), and $661 in the Philippines (110 drug-resistant). 99DOTS costs may be similar to or less expensive than standard DOT. VOT is more expensive, although in some settings, labor cost offsets or economies of scale may yield savings. 99DOTS and VOT may yield savings to local programs if donors cover infrastructure costs.

Environmental factors such as temperature, humidity, light, and CO2 influence plant growth, and unfavorable environmental conditions cause stress in plants, producing symptoms in their early growth stages. The increasing importance of optimizing crop management strategies has led to a rising demand for the precise evaluation of stress symptoms during early plant growth. Advanced technologies are transforming plant health monitoring through enabling image-based stress analysis. Machine learning (ML) models can effectively identify the important features and morphological changes connected with various stress conditions through the use of large datasets acquired from high-resolution plant images. Therefore, the objective of this study was to develop a method for classifying the early-stage stress symptoms of pepper seedlings and enabling their identification and quantification using image processing and a support vector machine (SVM). Two-week-old pepper seedlings were grown under different temperatures (20, 25, and 30 °C), light intensity levels (50, 250, and 450 µmol m−2s−1), and day–night hours (8/16, 10/14, and 16/8) in five controlled plant growth chambers. Images of the seedling canopies were captured daily using a low-cost red, green, and blue (RGB) camera over a two-week period. Eighteen color features, nine texture features using the gray-level co-occurrence matrix (GLCM), and one morphological feature were extracted from each image. A two-way ANOVA and multiple mean comparison (Duncan) analysis were used to determine the statistical significance of the treatment effects. To reduce feature overlap, sequential feature selection (SFS) was applied, and a support vector machine (SVM) was used for stress classification. The SFS method was used to identify the optimal features for the classification model, leading to substantial increases in stress classification accuracy. The SVM model, using these selected features, achieved a classification accuracy of 82% without the SFS and 86% with the SFS. To address overfitting, 5- and 10-fold cross-validation were used, resulting in MAEs of 0.138 and 0.163 for the polynomial kernel, respectively. The SVM model, evaluated with the ROC curve and confusion matrix, achieved a classification accuracy of 85%. This classification approach enables real-time stress monitoring, allowing growers to optimize environmental conditions and enhance seedling growth. Future directions include integrating this system into automated cultivation environments to enable continuous, efficient stress monitoring and response, further improving crop management and productivity.

The health monitoring of vegetable and fruit plants, especially during the critical seedling growth stage, is essential to protect them from various environmental stresses and prevent yield loss. Different environmental stresses may cause similar symptoms, making visual inspection alone unreliable and potentially leading to an incorrect diagnosis and delayed corrective actions. This study aimed to address these challenges by proposing a segmented regression model and a Mask R-CNN model for detecting the initiation time and symptoms of nutrient stress in cucumber seedlings within a controlled environment. Nutrient stress was induced by applying two different treatments: an indicative nutrient deficiency with an electrical conductivity (EC) of 0 dSm−1, and excess nutrients with a high-concentration nutrient solution and an EC of 6 dSm−1. Images of the seedlings were collected using an automatic image acquisition system two weeks after germination. The early initiation of nutrient stress was detected using a segmented regression analysis, which analyzed morphological and textural features extracted from the images. For the Mask R-CNN model, 800 seedling images were annotated based on the segmented regression analysis results. Nutrient-stressed seedlings were identified from the initiation day to 4.2 days after treatment application. The Mask R-CNN model, implemented using ResNet-101 for feature extraction, leveraged transfer learning to train the network with a smaller dataset, thereby reducing the processing time. This study identifies the top projected canopy area (TPCA), energy, entropy, and homogeneity as prospective indicators of nutritional deficits in cucumber seedlings. The results from the Mask R-CNN model are promising, with the best-fit image achieving an F1 score of 93.4%, a precision of 93%, and a recall of 94%. These findings demonstrate the effectiveness of the integrated statistical and machine learning (ML) methods for the early and accurate diagnosis of nutrient stress. The use of segmented regression for initial detection, followed by the Mask R-CNN for precise identification, emphasizes the potential of this approach to enhance agricultural practices. By facilitating the early detection and accurate diagnosis of nutrient stress, this approach allows for quicker and more precise treatments, which improve crop health and productivity. Future research could expand this methodology to other crop types and field conditions to enhance image processing techniques, and researchers may also integrate real-time monitoring systems.

Abstract Introduction One of the contributors to tuberculosis (TB) burden among vulnerable populations, such as sexual minority people, is the delay in case finding and notification. Given their socially excluded, hard-to-reach nature, community-led approaches need to be introduced to facilitate their screening of TB symptoms and their subsequent referral to TB healthcare providers. This article aimed to explore the existing challenges surrounding TB screening and referral, and the implementation facilitators and barriers of the proposed community-based TB screening model for sexual minority people in Dhaka, Bangladesh. Methods This study followed the quasi-experimental design using mixed methods (i.e., qualitative and quantitative) approach. The study participants who were also a part of the community-led TB screening model included sexual minority people enrolled in HIV prevention interventions. In addition to quantitative inquiry, in-depth interviews were conducted on sexual minority people, focus group discussions were also conducted on them and HIV prevention service providers, and key-informant interviews were conducted on service providers, programmatic experts and TB researchers. Data were analyzed using content, contextual and thematic approaches. Results The ‘Six Steps in Quality Intervention Development’ framework was used to guide the development of the community-based TB screening model. In Step 1 (identifying the problem), findings revealed low rates of TB screening among sexual minority people enrolled in the HIV prevention intervention. In Step 2 (identifying contextual factors for change), various individual, and programmatic factors were identified, which included low knowledge, low-risk perception, prioritization of HIV services over TB, and stigma and discrimination towards these populations. In Step 3 (deciding change mechanism), community-based screening approaches were applied, thus leading to Step 4 (delivery of change mechanism) which designed a community-based approach leveraging the peer educators of the HIV intervention. Step 5 (testing intervention) identified some barriers and ways forward for refining the intervention, such as home-based screening and use of social media. Step 6 (collecting evidence of effectiveness) revealed that the main strength was its ability to engage peer educators. Conclusion This study indicates that a community-based peer-led TB screening approach could enhance TB screening, presumptive TB case finding and referral among these populations. Therefore, this study recommends that this approach should be incorporated to complement the existing TB program.

ABSTRACT Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) continues to spread and evolve, giving rise to new surges in cases and deaths. Although nasopharyngeal swab (NPS) samples are the gold standard for diagnosing SARS-CoV2, NPS sampling is invasive and requires skilled staff, specialized transport medium, and nucleic acid extraction. The SalivaDirect method uses saliva samples and a simplified, flexible approach to overcome these drawbacks. In our study conducted at the COVID-19 Screening Unit of the Dhaka Hospital of icddr,b (International Centre for Diarrheal Disease Research, Bangladesh), the diagnostic performance of SalivaDirect and NPS was compared using paired samples. SARS-CoV2 was detected by performing RT-qPCR using RNA extracted from saliva samples with the SalivaDirect method and from the NPS with extracted RNA. A total of 200 participants were enrolled from February to March 2021, among whom 78 (39.0%) tested positive for SAR-CoV2 from at least one sample. Among the 78 participants testing positive, 65 (83.3%) tested positive in both specimens, eight (10.3%) tested positive only in NPS, and five (6.4%) tested positive only in saliva. SalivaDirect had a sensitivity of 89.0% and specificity of 96.1%, with NPS as the reference test. The sensitivity of NPS and SalivaDirect was 93.6% and 89.7% respectively, with a composite reference standard (where patients are defined as positive if tested positive in either method) as the reference. Our findings demonstrated that the SalivaDirect method can be used as an alternative to NPS in our clinical setting and also supports the use of SalivaDirect in other settings. IMPORTANCE Affordable and accessible tests for COVID-19 allow for timely disease treatment and pandemic management. SalivaDirect is a faster and easier method to implement than NPS sampling. Patients can self-collect saliva samples at home or in other non-clinical settings without the help of a healthcare professional. Sample processing in SalivaDirect is less complex and more adaptable than in conventional nucleic acid extraction methods. We found that SalivaDirect has good diagnostic performance and is ideal for large-scale testing in settings where supplies may be limited or trained healthcare professionals are unavailable.

Digital adherence technologies (DATs) have emerged as an alternative to directly observed therapy (DOT) for supervisions of tuberculosis (TB) treatment. We conducted a meta-analysis of implementation feedback obtained from people with TB and health care workers (HCWs) involved in TB REACH Wave 6-funded DAT evaluation projects. Projects administered standardized post-implementation surveys based on the Capability, Opportunity, Motivation, Behavior (COM-B) model to people with TB and their health care workers. The surveys included questions on demographics and technology use, Likert scale questions to assess capability, opportunity, and motivation to use DAT and open-ended feedback. We summarized demographic and technology use data descriptively, generated pooled estimates of responses to Likert scale questions within each COM-B category for people with TB and health care workers using random effects models, and performed qualitative analysis of open-ended feedback using a modified framework analysis approach. The analysis included surveys administered to 1290 people with TB and 90 HCWs across 6 TB REACH-funded projects. People with TB and HCWs had an overall positive impression of DATs with pooled estimates between 4·0 to 4·8 out of 5 across COM-B categories. However, 44% of people with TB reported taking TB medications without reporting dosing via DATs and 23% reported missing a dose of medication. Common reasons included problems with electricity, network coverage, and technical issues with the DAT platform. DATs were overall perceived to reduce visits to clinics, decrease cost, increase social support, and decrease workload of HCWs. DATs were acceptable in a wide variety of settings. However, there were challenges related to the feasibility of using current DAT platforms. Implementation efforts should concentrate on ensuring access, anticipating, and addressing technical challenges, and minimizing additional cost to people with TB.

Understanding the diverse environmental influences on seedling growth is critical for maximizing yields. The need for a more comprehensive understanding of how various environmental factors affect seedling growth is required. Integrating sensor data and image processing techniques offers a promising approach to accurately detect stress symptoms and uncover hidden patterns, enhancing the comprehension of seedling responses to environmental factors. The objective of this study was to quantify environmental stress symptoms for six seedling varieties using image-extracted feature characteristics. Three sensors were used: an RGB camera for color, shape, and size information; a thermal camera for measuring canopy temperature; and a depth camera for providing seedling height from the image-extracted features. Six seedling varieties were grown under controlled conditions, with variations in temperature, light intensity, nutrients, and water supply, while daily automated imaging was conducted for two weeks. Key seedling features, including leaf area, leaf color, seedling height, and canopy temperature, were derived through image processing techniques. These features were then employed to quantify stress symptoms for each seedling type. The analysis of stress effects on the six seedling varieties revealed distinct responses to environmental stressors. Integration of color, size, and shape parameters established a visual hierarchy: pepper and pak choi seedlings showed a good response, cucumber seedlings showed a milder response, and lettuce and tomato seedlings displayed an intermediate response. Pepper and tomato seedlings exhibited a wide range of growth stress symptoms, at 13.00% to 83.33% and 2.96% to 70.01%, respectively, indicating considerable variability in their reactions to environmental stressors. The suggested classification approach provides valuable groundwork for advancing stress monitoring and enabling growers to optimize environmental conditions.

Background: The World Health Organization is considering substituting Xpert MTB/RIF (Xpert) with Xpert MTB/RIF Ultra (Ultra) for tuberculosis (TB) diagnosis, but supportive evidence is scarce, particularly among people more likely (presumptive) to have paucibacillary pulmonary TB (PTB). Methods: During January-July 2018, presumptive PTB patients visiting TB Screening and Treatment Centres of Dhaka for routine chest X-ray (CXR) and conventional Xpert were enrolled. Sputum specimens were additionally tested with microscopy, culture, and Ultra. Specimens with “Trace call” by Ultra (Ultra-trace) were retested. Yield and diagnostic accuracy using various approaches to Ultra-trace and concordance of Ultra with bacteriological-positive PTB were assessed. Results: Altogether, 1,083 participants (104 ‘Xpert-positive’; 979 ‘Xpert-negative and CXR-suggestive’) were enrolled. All Xpert-positives and 900 (92%) Xpert-negatives were concordant with Ultra, however, seventy-nine (8.1%) Xpert-negative specimens tested positive with Ultra; 37 (46.8%) were categorically positives, and 42 (53.2%) were Ultra-trace. Sixteen of the 42 were retested, of whom eight (50.1%) Ultra-trace turned categorically positive, leading to 45 (4.6%) additionally detected by Ultra. Ultra sensitivity and specificity were 93.9% and 94.6%, and it additionally detected 5.4% more TB patients with a concordance of 94.6% (kappa, □=0.78) compared to any bacteriologically positive specimen (microscopy, culture, or Xpert). Conclusion: Ultra exhibited improved detection and accuracy among Xpert-negatives in a cohort with a high likelihood of PTB.

Bangladesh is a lower-middle-income country with a high burden of mental health conditions and inadequate health systems. Prior research in similar settings has found that training physicians in mental health literacy can contribute to reducing the mental health treatment gap and strengthening the mental health care pathway. This study explores the need for mental health training for physicians by gathering stakeholders’ perspectives and proposes recommendations for designing a mental training program in the context of Bangladesh.Key informant interviews were conducted among psychiatrists (n ​= ​9), and mental health entrepreneurs (n ​= ​7); one focus group discussion was conducted with psychologists (n ​= ​8); and one-on-one interviews were held with physician (n ​= ​17). Due to the COVID-19 restrictions, all interviews were conducted online, recorded and transcribed. Transcriptions were analyzed thematically, utilizing both an inductive and deductive approach.The data analysis from forty-one stakeholders generated three major themes and eight subthemes. Stakeholders perceived that the inadequate mental health system and low mental health awareness among physicians significantly contribute to the mental health treatment gaps. Stakeholders emphasized the need to include mental health training for physicians to increase skills related to identification and management of mental health conditions. Stakeholders suggested some basic components for the training content, feasible modalities to deliver the training, and implementation challenges. Recommendations included utilizing online training, ensuring interesting and practical content, and incorporating certification systems. At a systems level, stakeholders recommended including a mental health curriculum in undergraduate medical education, capacity building of other healthcare workers and increasing awareness at the policy level.There is clear agreement among stakeholders that implementing mental health training for physicians will promote universal health coverage and reduce the mental health treatment gap in Bangladesh. These findings can support creation of policies to strengthen the care pathway in countries with limited resources.

Accurate and appropriate extrapulmonary tuberculosis (EPTB) diagnosis remains challenging due to its paucibacillary nature, requirement of invasive collection procedures, and lack of sensitive tests. This study investigated the diagnostic performance of different methods for the diagnosis of EPTB. A total of 1340 EPTB specimens were collected from presumptive EPTB patients from four different hospitals between November 2015 and March 2017. The collected specimens were tested with AFB microscopy, culture, Xpert MTB/RIF assay (Xpert), and MTBDRplus assay. Among the 1340 EPTB specimens, 49 (3.66%), 141 (10.52%), 166 (12.39%), and 154 (11.49%) were positive in AFB microscopy, culture, Xpert MTB/RIF, and MTBDRplus assay, respectively. A total of 194 (14.9%) cases were found positive in at least one of these methods. Using culture as a reference standard, the sensitivity and specificity of AFB microscopy, Xpert MTB/RIF, and MTBDRplus assay were: 27.0%/99.1%, 83.7%/96.0%, and 79.4%/96.5%, respectively. Compared to the composite reference standard, the sensitivity of culture, AFB microscopy, Xpert MTB/RIF, and MTBDRplus assay was 72.7%, 25.3%, 85.6%, and 79.4%, respectively, with a specificity of 100% for all the methods. The Xpert MTB/RIF assay showed the highest sensitivity compared to other methods. Considering the short turnaround time and promising findings, Xpert MTB/RIF assay should be integrated into national TB guidelines as a routine diagnostic test.

Computer-aided detection (CAD) was recently recommended by the WHO for TB screening and triage based on several evaluations, but unlike traditional diagnostic tests, software versions are updated frequently and require constant evaluation. Since then, newer versions of two of the evaluated products have already been released. We used a case control sample of 12,890 chest X-rays to compare performance and model the programmatic effect of upgrading to newer versions of CAD4TB and qXR. We compared the area under the receiver operating characteristic curve (AUC), overall, and with data stratified by age, TB history, gender, and patient source. All versions were compared against radiologist readings and WHO's Target Product Profile (TPP) for a TB triage test. Both newer versions significantly outperformed their predecessors in terms of AUC: CAD4TB version 6 (0.823 [0.816-0.830]), version 7 (0.903 [0.897-0.908]) and qXR version 2 (0.872 [0.866-0.878]), version 3 (0.906 [0.901-0.911]). Newer versions met WHO TPP values, older versions did not. All products equalled or surpassed the human radiologist performance with improvements in triage ability in newer versions. Humans and CAD performed worse in older age groups and among those with TB history. New versions of CAD outperform their predecessors. Prior to implementation CAD should be evaluated using local data because underlying neural networks can differ significantly. An independent rapid evaluation centre is necessitated to provide implementers with performance data on new versions of CAD products as they are developed.

ABSTRACT Although the number of multidrug-resistant (MDR) tuberculosis (TB) cases is high overall, a major gap exists in our understanding of the molecular characteristics and transmission dynamics of the MDR Mycobacterium tuberculosis isolates circulating in Bangladesh. The present study aims to characterize the MDR-TB isolates of Bangladesh and to investigate the mode of transmission. A total of 544 MDR-TB isolates were obtained from a nationwide drug-resistant TB surveillance study conducted between October 2011 and March 2017 covering all geographic divisions of Bangladesh. The isolates were characterized using TbD1 deletion analysis, spoligotyping, and mycobacterial interspersed repetitive-unit–variable-number tandem-repeat (MIRU-VNTR) typing. Deletion analysis showed that 440 (80.9%) isolates were the modern type, while the remainder were the ancestral type. The largest circulating lineage was the Beijing type, comprising 208 isolates (38.2%), followed by T, EAI, and LAM with 93 (17.1%), 58 (10.7%), and 52 (9.5%) isolates, respectively. Combined MIRU-VNTR and spoligotyping analysis demonstrated that the majority of the clustered isolates were of the Beijing and T1 lineages. The overall rate of recent transmission was estimated at 33.8%. In conclusion, the MDR M. tuberculosis isolates circulating in Bangladesh are mostly of the modern virulent type. The Beijing and T lineages are the predominant types and most of the transmission of MDR-TB can be attributed to them. The findings also suggest that, along with the remarkable transmission, the emergence of MDR-TB in Bangladesh is largely due to acquired resistance. Rapid and accurate diagnosis and successful treatment will be crucial for controlling MDR-TB in Bangladesh. IMPORTANCE Multidrug-resistant TB is considered to be the major threat to tuberculosis control activities worldwide, including in Bangladesh. Despite the fact that the number of MDR-TB cases is high, a major gap exists in our understanding of the molecular epidemiology of the MDR-TB isolates in Bangladesh. In our study, we characterized and classified the MDR-TB isolates circulating in Bangladesh and investigated their mode of transmission. Our results demonstrated that the MDR M. tuberculosis isolates circulating in Bangladesh are mostly of the modern virulent type. The Beijing and T lineages are the predominant types and are implicated in the majority of MDR-TB transmission. Our findings reveal that, along with the remarkable transmission, the emergence of MDR-TB in Bangladesh is largely due to acquired resistance, which may be due to nonadherence to treatment or inadequate treatment of TB patients. Rapid diagnosis and adherence to an appropriate treatment regimen are therefore crucial to controlling MDR-TB in Bangladesh.

The COVID-19 pandemic has impacted health systems and health programs across the world. For tuberculosis (TB), it is predicted to set back progress by at least twelve years. Public private mix (PPM)has made a vital contribution to reach End TB targets with a ten-fold rise in TB notifications from private providers between 2012 and 2019. This is due in large part to the efforts of intermediary agencies, which aggregate demand from private providers. The COVID-19 pandemic has put these gains at risk over the past year. In this rapid assessment, representatives of 15 intermediary agencies from seven countries that are considered the highest priority for PPM in TB care (the Big Seven) share their views on the impact of COVID-19 on their programs, the private providers operating under their PPM schemes, and their private TB clients.All intermediaries reported a drop in TB testing and notifications, and the closure of some private practices. While travel restrictions and the fear of contracting COVID-19 were the main contributing factors, there were also unanticipated expenses for private providers, which were transferred to patients via increased prices. Intermediaries also had their routine activities disrupted and had to shift tasks and budgets to meet the new needs. However, the intermediaries and their partners rapidly adapted, including an increased use of digital tools, patient-centric services, and ancillary support for private providers.Despite many setbacks, the COVID-19 pandemic has underlined the importance of effective private sector engagement. The robust approach to fight COVID-19 has shown the possibilities for ending TB with a similar approach, augmented by the digital revolution around treatment and diagnostics and the push to decentralize health services.

ABSTRACT Coronavirus disease 19 (COVID-19)—caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)—has spread rapidly around the world. The global shortage of equipment and health care professionals, diagnostic cost, and difficulty in collecting nasopharyngeal swabs (NPSs) necessitate the use of an alternative specimen type for SARS-CoV-2 diagnosis. In this study, we investigated the use of saliva as an alternative specimen type for SARS-CoV-2 detection. Participants presenting COVID-19 symptoms and their contacts were enrolled at the COVID-19 Screening Unit of Dhaka Hospital of the International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), from July to November 2020. Paired NPS and saliva specimens were collected from each participant. Reverse transcription-quantitative PCR (RT-qPCR) was performed to detect SARS-CoV-2. Of the 596 suspected COVID-19-positive participants, 231 (38.7%) were detected as COVID-19 positive by RT-qPCR from at least 1 specimen type. Among the positive cases, 184 (79.6%) patients were identified to be positive for SARS-CoV-2 based on NPS and saliva samples, whereas 45 (19.65%) patients were positive for SARS-CoV-2 based on NPS samples but negative for SARS-CoV-2 based on the saliva samples. Two (0.5%) patients were positive for SARS-CoV-2 based on saliva samples but negative for SARS-CoV-2 based on NPS samples. The sensitivity and specificity of the saliva samples were 80.3% and 99.4%, respectively. SARS-CoV-2 detection was higher in saliva (85.1%) among the patients who visited the clinic after 1 to 5 days of symptom onset. A lower median cycle threshold (CT) value indicated a higher SARS-CoV-2 viral load in NPS than that in saliva for target genes among the positive specimens. The study findings suggest that saliva can be used accurately for diagnosis of SARS-CoV-2 early after symptom onset in clinical and community settings. IMPORTANCE As the COVID-19 pandemic erupted, the WHO recommended the use of nasopharyngeal or throat swabs for the detection of SARS-CoV-2 etiology of COVID-19. The collection of NPS causes discomfort because of its invasive collection procedure. There are considerable risks to health care workers during the collection of these specimens. Therefore, an alternative, noninvasive, reliable, and self-collected specimen was explored in this study. This study investigated the feasibility and suitability of saliva versus NPS for the detection of SARS-CoV-2. Here, we showed that the sensitivity of saliva specimens was 80.35%, which meets the WHO criteria. Saliva is an easy-to-get, convenient, and low-cost specimen that yields better results if it is collected within the first 5 days of symptom onset. Our study findings suggest that saliva can be used in low-resource countries, community settings, and vulnerable groups, such as children and elderly people.

Abstract Background The study was conducted to evaluate the analgesic, anti-inflammatory, antipyretic properties of ethanolic extract of Tacca integrifolia rhizome (EETI) in mice and cytotoxic effects in brine shrimp nauplii followed by a PASS prediction study for some isolated compounds of T. integrifolia. Additionally, this experiment included the in silico molecular docking and ADME/T property analyses of some phytochemicals. Methods Formalin- induced paw licking test and acetic acid-induced writhing test for analgesic activity, carrageenan-induced paw edema test for anti-inflammatory potential and Brewer’s yeast-induced pyrexia test for antipyretic activity were applied. Antinociceptive and antineoplastic activity for breast cancer were revealed with PASS program. Schrodinger suite 2015 was used to evaluate the binding interaction and ADME/T properties of selected phytoconstituents with estrogen receptor alpha. Results In formalin-induced paw licking test, EETI at the doses of 200 and 400 mg/kg BW showed highly significant inhibition of writhing in both neurogenic and inflammatory phases. While EETI also exhibited highly significant, compared to control, writhing inhibition for both the doses in acetic acid-induced writhing test. Moderate anti-inflammatory effect at a dose of 400 mg/kg BW was noticed in paw-edema test. It also showed 77.51% of maximum antipyretic effect which was significantly effective compared to standard drug paracetamol (150 mg/kg) in Brewer’s yeast-induced pyrexia test. The EETI showed potential cytotoxic activity with LC50 value of 114.46 μg/mL. The PASS prediction revealed the potential antinociceptive and antineoplastic activity of target compounds. The compounds betulinic acid, quercetin-3-α-arabinoside, catsanogenin were found to be effective in molecular docking study. Conclusion It is evident that the EETI possesses highly significant analgesic activity with remarkable anti-inflammatory and antipyretic activity. The phytoconstituents have potential antinociceptive and antineoplastic (breast cancer) activity. Graphical abstract

Solar mini-grids are the solution of choice for the electrification of remote off grid communities across the world. However, studies of comparative performance evaluation of such mini-grids are limited. In this article, we propose performance parameters for off grid distributed electricity generation systems like solar mini-grids, and on this basis evaluate the performance of 21 solar mini-grids which have been in operational in Bangladesh for at least a year, using a two stage Data Envelopment Analysis approach. We look at the efficiencies in terms of project costs, land cost, storage capacity, number of customers served, consumption per customer, rated capacity, power generation, distribution network and annual power consumption. Our findings indicate that all the mini-grids are installed in a relatively cost effective way. However, the market potential in the mini-grid sites is often underestimated or overestimated, leading to inefficiencies. The sensitivity analysis of the models has also been conducted. The effects of uncontrollable factors like solar irradiation, panel efficiency, panel costs, land costs, solar home system penetration and share of commercial users are tested using Tobit models. All these factors except competition from solar home systems affect the efficiencies of the mini-grids. This study is the first to provide a benchmark based comparative analysis of off-grid solar mini-grids, proposing financial and technical performance parameters specifically applicable to the off-grid context.

In response to the World Health Organization (WHO) recommendation to reduce healthcare workers' (HCWs') exposure to tuberculosis (TB) in health settings, congregate settings, and households, the national TB control program of Bangladesh developed guidelines for TB infection prevention and control (IPC) in 2011. This study aimed to assess the implementation of the TB IPC healthcare measures in health settings in Bangladesh. Between February and June 2018, we conducted a mixed-method study at 11 health settings. The team conducted 59 key-informant interviews with HCWs to understand the status of and barriers impeding the implementation of the TB IPC guidelines. The team also performed a facility assessment survey and examined TB IPC practices. Most HCWs were unaware of the national TB IPC guidelines. There were no TB IPC plans or committees at the health settings. Further, a presumptive pulmonary TB patient triage checklist was absent in all health settings. However, during facility assessment, we observed patient triaging and separation in the TB specialty hospitals. Routine cough-etiquette advice was provided to the TB patients mentioned during the key-informant interviews, which was consistent with findings from the survey. This study identified poor implementation of TB IPC measures in health settings. Limited knowledge of the guidelines resulted in poor implementation of the recommendations. Interventions focusing on the dissemination of the TB IPC guidelines to HCWs along with regular training may improve compliance. Such initiatives should be taken by hospital senior leadership as well as national policy makers.

BackgroundRapid and early detection of drug susceptibility among multidrug-resistant tuberculosis (MDR-TB) patients could guide the timely initiation of effective treatment and reduce transmission of drug-resistant TB. In the current study, we evaluated the diagnostic performance of GenoType MTBDRsl (MTBDRsl) ver1.0 assay for detection of resistance to ofloxacin (OFL), kanamycin (KAN) and ethambutol (EMB), and additionally the XDR-TB among MDR-TB patients in Bangladesh.MethodsThe MTBDRsl assay was performed directly on 218 smear-positive sputum specimens collected from MDR-TB patients and the results were compared with the phenotypic drug susceptibility testing (DST) performed on solid Lowenstein-Jensen (L-J) media. We also analyzed the mutation patterns of gyrA, rrs, and embB genes for detection of resistance to OFL, KAN and EMB, respectively.ResultsThe sensitivity and specificity of the MTBDRsl compared to phenotypic L-J DST were 81.8% (95% CI, 69.1-90.9) and 98.8% (95% CI, 95.6-99.8), respectively for OFL (PPV: 95.7% & NPV: 94.1%); 65.1% (95% CI, 57.5-72.2) and 86.7% (95% CI, 73.2-94.9), respectively for EMB (PPV: 94.9% & NPV: 39.4%); and 100% for KAN. The diagnostic accuracy of KAN, OFL and EMB were 100, 94.5 and 69.6%, respectively. Moreover, the sensitivity, specificity and diagnostic accuracy of MtBDRsl for detection of XDR-TB was 100%. The most frequently observed mutations were at codon D94G (46.8%) of gyrA gene, A1401G (83.3%) of rrs gene, and M306V (41.5%) of the embB gene.ConclusionConsidering the excellent performance in this study we suggest that MTBDRsl assay can be used as an initial rapid test for detection of KAN and OFL susceptibility, as well as XDR-TB directly from smear-positive sputum specimens of MDR-TB patients in Bangladesh.

BackgroundIn recent non-pandemic periods, tuberculosis (TB) has been the leading killer worldwide from a single infectious disease. Patients with DM are three times more likely to develop active TB and poor treatment outcomes. Single glycemic measurements at TB diagnosis may inaccurately diagnose or mischaracterize DM severity. Data are limited regarding glycemic dynamics from TB diagnosis through treatment.MethodsProspective study of glycemia dynamics in response to TB treatment measured glycosylated haemoglobin (HbA1c) in patients presenting to TB screening centres in Bangladesh to determine the prevalence and risk factors of hyperglycemia before and at TB treatment completion.Results429 adults with active TB disease were enrolled and divided into groups based on history of DM and initial HbA1c range: normoglycemia, prediabetes, and DM. DM was diagnosed in 37%. At treatment completion,14(6%) patients from the normoglycemia and prediabetes groups had HbA1c>6.5%, thus increasing the prevalence of DM to 39%. The number needed to screen to diagnose one new case of DM at TB diagnosis was 5.7 and 16 at treatment completion in the groups without DM. Weight gain>5% at treatment completion significantly increased the risk of hyperglycemia in the groups without DM at TB diagnosis (95% CI 1.23-26.04, pConclusionHbA1c testing prior to and at TB treatment completion found a high prevalence of prediabetes and DM, including a proportion found at treatment completion and commonly in people with a higher percentage of weight gain. Further longitudinal research is needed to understand the effects of TB disease and treatment on insulin resistance and DM complications.

Background: Countries have introduced a variety of measures to prevent and treat COVID-19 with medicines and personal protective equipment (PPE), with some countries adopting preventative strategies earlier than others. However, there has been considerable controversy surrounding some treatments. This includes hydroxychloroquine where the initial hype and misinformation lead to shortages, price rises and suicides. Price rises and shortages have also been seen for PPE. Such activities can have catastrophic effects on patients where there are high co-payment levels and issues of affordability. Consequently, there is a need to investigate this further.Objective: Assess changes in the availability, utilization and prices of relevant medicines and PPE during the pandemic among a range of Asian countries.Our approach: Narrative literature review combined with interviews among community pharmacists to assess changes in consumption, prices and shortages of medicines and PPE from the beginning of March 2020 until end of May 2020. In addition, suggestions on ways to reduce misinformation.Results: 308 pharmacists took part from five Asian countries. There was an appreciable increase in the utilization of antimicrobials in Pakistan (in over 88% of pharmacies), with lower increases or no change in Bangladesh, India, Malaysia and Vietnam. Encouragingly, there was increased use of vitamins/immune boosters and PPE across the countries, as well as limited price rises for antimicrobials in India, Malaysia and Vietnam, although greater price rises seen for analgesics and vitamin C/immune boosters. Appreciable price increases were also seen for PPE across some countries.Conclusion: Encouraging to see increases in utilization of vitamins/immune boosters and PPE. However, increases in the utilization and prices of antimicrobials is a concern that needs addressing alongside misinformation and any unintended consequences from the pandemic. Community pharmacists can play a key role in providing evidence-based advice, helping to moderate prices, as well as helping address some of the unintended consequences of the pandemic.

Introduction Although Bangladesh is a country of generalised tuberculosis (TB) epidemic, the HIV prevalence is low among general populations, and 3.9% among key populations. Despite the high possibility of HIV–TB coinfection, scientifically tested approaches for increasing TB case detection among sexual minority people are yet to be developed and implemented in Bangladesh. Such approaches could foster service delivery linkages between communities and the government health system. Findings of this experimental research are likely to provide new insights for programme managers and policy planners for adopting a similar approach in order to enhance TB referral, thus ultimately increasing TB case detections and reducing the likelihood of TB-related mortalities and morbidities, irrespective of HIV status.Methods and analysis This operational research will follow a quasi-experimental design, applying both qualitative and quantitative methods, in two drop-in centres in three phases. Phase 1 will encompass baseline data collection and development of a community-based TB screening approach. In phase 2, the newly developed intervention will be implemented, followed by end-line data collection in phase 3. Qualitative data collection will be continued throughout the first and second phases. The baseline and end-line data will be compared both in the intervention and comparison areas to measure the impact of the intervention.Ethics and dissemination Ethical approval was obtained from the Institutional Review Board of International Centre for Diarrhoeal Disease Research, Bangladesh. The findings will be disseminated through diverse scientific forums including peer-reviewed journals, presentation at conferences and among the policy-makers for policy implication. The study started in January 2019 and will continue until June 2020.

BackgroundIn Bangladesh, about 80% of healthcare is provided by the private sector. Although free diagnosis and care is offered in the public sector, only half of the estimated number of people with tuberculosis are diagnosed, treated, and notified to the national program. Private sector engagement strategies often have been small scale and time limited. We evaluated a Social Enterprise Model combining external funding and income generation at three tuberculosis screening centres across the Dhaka Metropolitan Area for diagnosing and treating tuberculosis.Methods and findingsThe model established three tuberculosis screening centres across Dhaka Metropolitan Area that carried the icddr,b brand and offered free Xpert MTB/RIF tests to patients visiting the screening centres for subsidized, digital chest radiographs from April 2014 to December 2017. A network of private and public health care providers, and community recommendation was formed for patient referral. No financial incentives were offered to physicians for referrals. Revenues from radiography were used to support screening centres' operation. Tuberculosis patients could choose to receive treatment from the private or public sector. Between 2014 and 2017, 1,032 private facilities networked with 8,466 private providers were mapped within the Dhaka Metropolitan Area. 64, 031 patients with TB symptoms were referred by the private providers, public sector and community residents to the three screening centres with 80% coming from private providers. 4,270 private providers made at least one referral. Overall, 10,288 pulmonary and extra-pulmonary tuberculosis cases were detected and 7,695 were bacteriologically positive by Xpert, corresponding to 28% of the total notifications in Dhaka Metropolitan Area.ConclusionThe model established a network of private providers who referred individuals with presumptive tuberculosis without financial incentives to icddr,b's screening centres, facilitating a quarter of total tuberculosis notifications in Dhaka Metropolitan Area. Scaling up this approach may enhance national and international tuberculosis response.

The fast and accurate detection of susceptibility in drugs is a major challenge for a successful tuberculosis (TB) control programme. This study evaluated the performance of WHO-endorsed rapid diagnostic tools, such as BACTEC MGIT 960 SIRE (MGIT SIRE), GenoType MTBDRplus (MTBDRplus) and Xpert MTB/RIF (Xpert), for detecting susceptibility to first-line anti-TB drugs among pulmonary TB patients in Bangladesh. A total of 825 sputum samples with results from drug susceptibility testing (DST) against first-line anti-TB drugs in the MGIT SIRE, MTBDRplus and Xpert assays were evaluated and compared with the gold standard proportion susceptibility method of the Lowenstein–Jensen (LJ) medium. The overall sensitivities of MGIT SIRE were 97.6%, 90.0%, 61.3% and 44.9%, while specificities were 89.9%, 94.5%, 91.3% and 92.2% for detection of susceptibility to isoniazid (INH), rifampicin (RIF), streptomycin (STR) and ethambutol (EMB), respectively. For MTBDRplus, the sensitivities were 88.0% and 88.7%, and the specificities were 97.4% and 97.8% for the detection of susceptibility to INH and RIF, respectively. Xpert demonstrated a sensitivity and specificity of 94.8% and 99.5%, respectively, for the detection of RIF susceptibility. All tests performed significantly better in retreated TB patients compared with primary TB cases. For detection of RIF and INH susceptibility, all three assays showed almost perfect agreement with the LJ method, although MGIT SIRE exhibited low agreement for STR and EMB. Considering the high performance, shorter turnaround time and ease of use, molecular-based approaches Xpert and MTBDRplus can be widely implemented throughout the country for the rapid detection of drug-resistant TB.

Background: Emerging evidence suggests that several trace elements such as serum chromium (Cr) and selenium (Se) levels are altered in type 2 DM and its deficiencies are associated with the development of diabetes related complications. Objective: To assess the serum Cr and Se levels in patients of type 2 diabetes mellitus. Methods: This cross sectional study was conducted in the Department of Physiology, Dhaka Medical College, Dhaka from July 2014 to June 2015. Fifty type 2 diabetic patients with age ranging from 40 to 55 years were study group and fifty ages, BMI matched healthy subjects were control group. Patients were selected from Bangladesh Institute of Research for Diabetic Endocrine and Metabolic Disorders (BIRDEM) General Hospital, Dhaka. Serum Cr and Se levels were estimated by flame atomic absorption spectrophotometry. For statistical analysis unpaired Student’s‘t’ test and Chi square test were performed. Results: In this study, serum Cr and Se levels were significantly (P

Fluoroquinolone (FQ) compounds—moxifloxacin (MOX), levofloxacin (LEV), and ofloxacin (OFL)—are used to treat multidrug-resistant tuberculosis (MDR-TB) globally. In this study, we investigated the correlation of gyr mutations among Mtb isolates with the MICs of MOX, LEV, and OFL in Bangladesh. A total of 50 MDR-TB isolates with gyr mutations, detected by the GenoType MTBDRsl assay, were subjected to drug susceptibility testing to determine the MICs of the FQs. Spoligotyping was performed to correlate the genetic diversity of the gyr mutant isolates with different MIC distributions. Among the 50 isolates, 44 (88%) had mutations in the gyrA gene, one (2%) had a mutation in the gyrB gene, and five (10%) isolates had unidentified mutations. The substitutions in the gyrA region were at A90V (n = 19, 38%), D94G (n = 16, 32%), D94A (n = 4, 8%), D94N/D94Y (n = 4, 8%), and S91P (n = 1, 2%), compared to the gyrB gene at N538D (n = 1.2%). D94G mutations showed the highest MICs for MOX, LEV, and OFL, ranging between 4.0 and 8.0 μg/mL, 4.0 and 16.0 μg/mL, and 16.0 and 32.0 μg/mL, respectively; while the most common substitution of A90V showed the lowest ranges of MICs (1.0–4.0 μg/mL, 2.0–8.0 μg/mL, and 4.0–32.0 μg/mL, respectively). Spoligotyping lineages demonstrated no significant differences regarding the prevalence of different gyr mutations. In conclusion, the substitutions of codon A90V and D94G in the gyr genes were mostly responsible for the FQs’ resistance among Mtb isolates in Bangladesh. Low levels of resistance were associated with the substitutions of A90V, while the D94G substitutions were associated with a high level of resistance to all FQs.

Background: Due to large number of vehicles, air pollution is increasing day by day in Dhaka city. Automobile exhaust cause acute and chronic respiratory disease in traffic policemen as they are exposed to air pollution for prolong period of time. Objective: To observe the effect of long term exposure to air pollution on FVC, FEV1 and FEV1/FVC% of traffic policemen. Methods: This cross sectional study was conducted in the Department of Physiology, Dhaka Medical College (DMC), Dhaka from July 2014 to June 2015. Fifty apparently healthy traffic policemen with the age 25 to 45 years were selected as study group. Fifty age and BMI matched healthy male subjects were selected as control. The study subjects were selected from different traffic junctions and the control from different offices of Dhaka city. FVC, FEV1 and FEV1/FVC% of all the subjects were measured by a digital spirometer. Statistical analysis was done by Independent sample ‘t’ test. Results: In this study FVC, FEV1 and FEV1/FVC were significantly (p< 0.001) lower in the traffic policemen than the control group. Conclusion: From the result of this study it can be concluded that prolonged exposure to air pollution may decrease pulmonary function of the traffic policemen in Dhaka city.

With an increasing fatality rate, severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has emerged as a promising threat to human health worldwide. Recently, the World Health Organization (WHO) has announced the infectious disease caused by SARS-CoV-2, which is known as coronavirus disease-2019 (COVID-2019), as a global pandemic. Additionally, the positive cases are still following an upward trend worldwide and as a corollary, there is a need for a potential vaccine to impede the progression of the disease. Lately, it has been documented that the nucleocapsid (N) protein of SARS-CoV-2 is responsible for viral replication and interferes with host immune responses. We comparatively analyzed the sequences of N protein of SARS-CoV-2 for the identification of core attributes and analyzed the ancestry through phylogenetic analysis. Subsequently, we predicted the most immunogenic epitope for the T-cell and B-cell. Importantly, our investigation mainly focused on major histocompatibility complex (MHC) class I potential peptides and NTASWFTAL interacted with most human leukocyte antigen (HLA) that are encoded by MHC class I molecules. Further, molecular docking analysis unveiled that NTASWFTAL possessed a greater affinity towards HLA and also available in a greater range of the population. Our study provides a consolidated base for vaccine design and we hope that this computational analysis will pave the way for designing novel vaccine candidates.

BACKGROUND:The Xpert MTB/RIF (Xpert) assay technology allows rapid and sensitive diagnosis of pulmonary tuberculosis (PTB) from sputum specimens. However, diagnosis of PTB is difficult for patients who cannot produce sputum. The objective of this study was to investigate the use of Xpert assay for successful detection of PTB using stool samples from adult subjects. METHODS:Both stool and sputum samples from known smear and Xpert positive PTB patients were collected from a TB hospital in Dhaka. Stool samples were collected from healthy individuals without TB symptoms from a slum area of Dhaka. Stool and sputum samples were decontaminated and concentrated using NALC-NaOH-Na-citrate solution and the resultant sediment was used for Xpert, acid-fast bacilli (AFB) microscopy and culture. RESULTS:A total of 102 stool samples were collected from PTB patients and another 50 stool samples from healthy individuals without TB. The sensitivity of the Xpert assay for detection of M. tuberculosis in stool samples of PTB patients was 90.2% (95% CI, 82.9-95.0). All 50 stool samples from healthy individuals were negative by the assay (Specificity 100%; 95% CI, 92.9-100). Compared with the sputum culture positive results the sensitivity of the stool Xpert assay was 94.8% (95% CI, 88.5-97.8). Moreover, stool Xpert demonstrated full concordant results with the sputum culture for detection of rifampicin susceptibility. The cycle threshold values of rpoB probes obtained from Xpert assay correlated significantly with the bacilli load in the corresponding stool (Spearman correlation = -0.40, P < 0.01) and sputum (Spearman correlation = -0.77, P < 0.01) samples as determined by microscopy. CONCLUSIONS:Stool Xpert can be applied as a potential alternative of sputum testing for detection of M. tuberculosis and accurate determination of RIF susceptibility in adult PTB patients. The assay would be beneficial for rapid diagnosis of PTB for those adult patients who cannot expectorate sputum.

Culture based phenotypic drug susceptibility testing (DST) for Mycobacterium tuberculosis (TB) is time consuming therefore rapid genotypic methods are increasingly being utilized. We previously developed and evaluated on TB isolates a rapid genotypic TaqMan array card (TAC) that detects mutations in several resistance-associated genes using dozens of primer pairs, probes, and high resolution melt analysis, with >96% accuracy versus Sanger sequencing. In this study we examined the performance of TAC on sputum, comparing results between 71 paired sputum and TB isolates of which 62 were MDR-TB. We also adapted the TAC to include wild-type probes and broadened coverage for rpoB and gyrA mutations. TAC was 89% successful at detecting wild-type or mutations within inhA, katG, rpoB, eis, gyrA, rplC, and pncA on smear positive sputa and 33% successful on smear negative sputa. The overall accuracy of these detections as compared to the TAC results of the paired isolate was 95% ± 7 (average sensitivity 98% ± 3; specificity 92% ± 14). Accuracy of sputum TAC results versus phenotypic DST for isoniazid, rifampin, ofloxacin/moxifloxacin, and pyrazinamide was 85% ± 12. This was similar to that of the isolate TAC results (accuracy 88% ± 13), thus inaccuracies primarily reflected intrinsic genotypic-phenotypic discordance. The TAC is a rapid, modular, comprehensive, and accurate TB DST for the major first and second line TB drugs and could be used for supplemental testing of GeneXpert resistant smear positive sputum.

BACKGROUND:GeneXpert MTB/RIF (Xpert) and Genotype MTBDRplus (DRplus) are two World Health Organization (WHO) endorsed probe based molecular drug susceptibility testing (DST) methods for rapid diagnosis of drug resistant tuberculosis. Both methods target the same 81 bp Rifampicin Resistance Determining Region (RRDR) of bacterial RNA polymerase β subunit (rpoB) for detection of Rifampicin (RIF) resistance associated mutations using DNA probes. So there is a correspondence of the probes of each other and expected similarity of probe binding. METHODS:We analyzed 92 sputum specimens by Xpert, DRplus and LJ proportion method (LJ-DST). We compared molecular DSTs with gold standard LJ-DST. We wanted to see the agreement level of two molecular methods for detection of RIF resistance associated mutations. The 81bp RRDR region of rpoB gene of discrepant cases between the two molecular methods was sequenced by Sanger sequencing. RESULTS:The agreement of Xpert and DRplus with LJ-DST for detection of RIF susceptibility was found to be 93.5% and 92.4%, respectively. We also found 92.4% overall agreement of two molecular methods for the detection of RIF susceptibility. A total of 84 out of 92 samples (91.3%) had agreement on the molecular locus of RRDR mutation by DRplus and Xpert. Sanger sequencing of 81bp RRDR revealed that Xpert probes detected seven of eight discrepant cases correctly and DRplus was erroneous in all the eight cases. CONCLUSION:Although the overall concordance with LJ-DST was similar for both Xpert and DRplus assay, Xpert demonstrated more accuracy in the detection of RIF susceptibility for discrepant isolates compared with DRplus. This observation would be helpful for the improvement of probe based detection of drug resistance associated mutations especially rpoB mutation in M. tuberculosis.

Multidrug-resistant tuberculosis (MDR-TB) treatment in Bangladesh is empiric or based on qualitative drug-susceptibility testing (DST) by comparative growth in culture media with and without a single drug concentration.Adult patients were enrolled throughout Bangladesh during the period of 2011-2013 at MDR-TB treatment initiation. Quantitative DST by minimum inhibitory concentration (MIC) testing for 12 first and second-line anti-TB drugs was compared to pretreatment clinical characteristics and treatment outcomes. MIC values at or one dilution lower than the resistance breakpoint used for qualitative DST were categorized as borderline susceptible, and MIC values one or two dilutions greater as borderline resistant.Seventy-four patients were enrolled with a mean age of 35 ± 15 years, and 51 (69%) were men. Of the rifampin isolates with MIC >1.0 μg/ml, 12 (19%) were fully susceptible or borderline susceptible to rifabutin (MIC ≤ 0.5 μg/ml). Amikacin was fully susceptible in 73 isolates (99%), but kanamycin in only 54 (75%) (p